/EXTERNAL Roadmap/variants/K006559_K006560_K006561_K006562_K006563_5_lane_gembs
BACK
SAMPLE K006559_K006560_K006561_K006562_K006563_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1177462436 |
717093361 |
60.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1177462436 |
100% |
1128506249 |
95.84 % |
48956187 |
4.16 % |
| |
|
|
|
|
|
|
| Passed |
720945287 |
61.23 % |
713000432 |
63.18 % |
7944855 |
1.10 % |
| Filtered |
456517149 |
38.77 % |
415505817 |
36.82 % |
41011332 |
5.69 % |
| |
|
|
|
|
|
|
| q20 |
300770398 |
65.88 % |
285367153 |
68.68 % |
15403245 |
37.56 % |
| q20,mq40 |
74792955 |
16.38 % |
72368430 |
17.42 % |
2424525 |
5.91 % |
| q20,qd2 |
31008846 |
6.79 % |
11650490 |
2.80 % |
19358356 |
47.20 % |
| mq40 |
30990425 |
6.79 % |
29478012 |
7.09 % |
1512413 |
3.69 % |
| qd2 |
9375981 |
2.05 % |
8967988 |
2.16 % |
407993 |
0.99 % |
| q20,qd2,mq40 |
9364351 |
2.05 % |
7490778 |
1.80 % |
1873573 |
4.57 % |
| qd2,mq40 |
210111 |
0.05 % |
182966 |
0.04 % |
27145 |
0.07 % |
| fs60 |
1836 |
0.00 % |
0 |
0.00 % |
1836 |
0.00 % |
| fs60,mq40 |
1600 |
0.00 % |
0 |
0.00 % |
1600 |
0.00 % |
| q20,qd2,fs60 |
165 |
0.00 % |
0 |
0.00 % |
165 |
0.00 % |
| q20,qd2,fs60,mq40 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| qd2,fs60 |
144 |
0.00 % |
0 |
0.00 % |
144 |
0.00 % |
| qd2,fs60,mq40 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| q20,fs60,mq40 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
17059719 |
33.46 % |
| Transition |
G>A |
All |
2666411 |
5.23 % |
| Transition |
T>C |
All |
20882787 |
40.96 % |
| Transition |
C>T |
All |
2380633 |
4.67 % |
| Transversion |
A>C |
All |
1021049 |
2.00 % |
| Transversion |
C>A |
All |
1074648 |
2.11 % |
| Transversion |
T>G |
All |
1157519 |
2.27 % |
| Transversion |
G>T |
All |
1072469 |
2.10 % |
| Transversion |
A>T |
All |
920398 |
1.81 % |
| Transversion |
T>A |
All |
906014 |
1.78 % |
| Transversion |
C>G |
All |
982668 |
1.93 % |
| Transversion |
G>C |
All |
855178 |
1.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1246276 |
26.31 % |
| Transition |
G>A |
Passed |
386380 |
8.16 % |
| Transition |
T>C |
Passed |
1754420 |
37.04 % |
| Transition |
C>T |
Passed |
392692 |
8.29 % |
| Transversion |
A>C |
Passed |
139059 |
2.94 % |
| Transversion |
C>A |
Passed |
104795 |
2.21 % |
| Transversion |
T>G |
Passed |
150760 |
3.18 % |
| Transversion |
G>T |
Passed |
105617 |
2.23 % |
| Transversion |
A>T |
Passed |
93444 |
1.97 % |
| Transversion |
T>A |
Passed |
93539 |
1.98 % |
| Transversion |
C>G |
Passed |
139242 |
2.94 % |
| Transversion |
G>C |
Passed |
129897 |
2.74 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
5.38 |
42989550 |
7989943 |
| Passed |
3.95 |
3779768 |
956353 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |